VANANZ dynamic cytotoxicity: parsing PI kinetics data
Stefano Giulieri
06/10/2019
library(tidyverse)
library(magrittr)
rm(list = ls())Create the file structure for the first 5 plates
# plates and experiments
plate2 <- c(
"exp_190831",
"exp_190905",
"exp_190909",
"exp_190921",
"exp_191107"
)
plate3 <- c(
"exp_190923",
"exp_191109",
"exp_191111"
)
plate1 <- c(
"exp_191115",
"exp_191116"
)
plate4 <- c(
"exp_191120",
"exp_191121"
)
plate5 <- c(
"exp_191129",
"exp_191130"
)
plate_exp_list <- list(plate1, plate2, plate3, plate4, plate5)
names(plate_exp_list) <- sapply(1:5, function(x){
str_c("plate", x)
})
# folders
folders <- c(
"Growth_curves",
"Inocula_OD",
"LDH",
"PI_endpoints",
"PI_kinetics",
"Parameters"
)
# Generate file structure
directories <- sapply(1:length(plate_exp_list), function(i){
dir <- str_c("Raw_data/", names(plate_exp_list[i]))
if (!dir.exists(dir)) dir.create(dir)
directories <-sapply(plate_exp_list[[i]], function(x){
dir <- str_c(dir, "/", x)
if (!dir.exists(dir)) dir.create(dir)
return(dir)
})
return(directories)
})
# Move existing data manually
# plate2 <- c(
# "exp_190831",
# "exp_190905",
# "exp_190909",
# "exp_190921",
# "exp_191107"
# )
# plate3 <- c(
# "exp_190923",
# "exp_191109",
# "exp_191111"
# )
# plate1 <- c(
# "exp_191115",
# "exp_191116"
# )
# Create folder structure
# vector of directories
directories <- Reduce(c, directories)
purrr::walk(directories, function(x){
lapply(folders, function(y){
dir <- str_c(x, "/", y)
print(str_c("Checking if ", dir, "exists ..."))
if (!dir.exists(dir)) dir.create(dir)
})
})## [1] "Checking if Raw_data/plate1/exp_191115/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate1/exp_191115/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate1/exp_191115/LDHexists ..."
## [1] "Checking if Raw_data/plate1/exp_191115/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate1/exp_191115/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate1/exp_191115/Parametersexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/LDHexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate1/exp_191116/Parametersexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/LDHexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190831/Parametersexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/LDHexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190905/Parametersexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/LDHexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190909/Parametersexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/LDHexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate2/exp_190921/Parametersexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/LDHexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate2/exp_191107/Parametersexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/LDHexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate3/exp_190923/Parametersexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/LDHexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate3/exp_191109/Parametersexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/LDHexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate3/exp_191111/Parametersexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/LDHexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate4/exp_191120/Parametersexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/LDHexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate4/exp_191121/Parametersexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/LDHexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate5/exp_191129/Parametersexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/Growth_curvesexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/Inocula_ODexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/LDHexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/PI_endpointsexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/PI_kineticsexists ..."
## [1] "Checking if Raw_data/plate5/exp_191130/Parametersexists ..."PI kinetics
Import raw data, one table at the time
source("Functions/parse_results.R")experiment 190831
# arguments for parse function
file <- "Raw_data/plate2/exp_190831/PI_kinetics/190831 LD PI Assay VANANZ 24 hours.xlsx"
duration <- c(22, 42)
wavelength <- c(493, 535)
# new variables
exp <- "exp190831"
cell_number <- 40e3
plate <- 2
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,888 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A01 21309 0 A 01 exp190831 40000 2
## 2 A02 20923 0 A 02 exp190831 40000 2
## 3 A03 19649 0 A 03 exp190831 40000 2
## 4 A04 20962 0 A 04 exp190831 40000 2
## 5 A05 20381 0 A 05 exp190831 40000 2
## 6 A06 20933 0 A 06 exp190831 40000 2
## 7 A07 20737 0 A 07 exp190831 40000 2
## 8 A08 21094 0 A 08 exp190831 40000 2
## 9 A09 20141 0 A 09 exp190831 40000 2
## 10 A10 20781 0 A 10 exp190831 40000 2
## # … with 21,878 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data <- list()
kinetics_data[[1]] <- dataexp 090905
file <- "Raw_data/plate2/exp_190905/PI_kinetics/190830 HeLa 25000 Cell death rate dynamic.xlsx"
duration <- c(20, 6)
wavelength <- c(493, 535)
# new variables
exp <- "exp190905"
cell_number <- 25e3
plate <- 2
# parse results
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 19,392 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A01 1132 0 A 01 exp190905 25000 2
## 2 A02 1123 0 A 02 exp190905 25000 2
## 3 A03 1143 0 A 03 exp190905 25000 2
## 4 A04 1119 0 A 04 exp190905 25000 2
## 5 A05 1135 0 A 05 exp190905 25000 2
## 6 A06 1130 0 A 06 exp190905 25000 2
## 7 A07 1122 0 A 07 exp190905 25000 2
## 8 A08 1139 0 A 08 exp190905 25000 2
## 9 A09 1127 0 A 09 exp190905 25000 2
## 10 A10 1140 0 A 10 exp190905 25000 2
## # … with 19,382 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[2]] <- dataexp 190909
file <- "Raw_data/plate2/exp_190909/PI_kinetics/190910.Plate.Vananz.2.HeLa.20000.cell.death.rate.dynamic.run.3.xlsx"
duration <- c(21, 0)
wavelength <- 535
# new variables
exp <- "exp190909"
cell_number <- 20e3
plate <- 2
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 20,256 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A01 27434 0 A 01 exp190909 20000 2
## 2 A02 27092 0 A 02 exp190909 20000 2
## 3 A03 27328 0 A 03 exp190909 20000 2
## 4 A04 27807 0 A 04 exp190909 20000 2
## 5 A05 28502 0 A 05 exp190909 20000 2
## 6 A06 28460 0 A 06 exp190909 20000 2
## 7 A07 29114 0 A 07 exp190909 20000 2
## 8 A08 28506 0 A 08 exp190909 20000 2
## 9 A09 27791 0 A 09 exp190909 20000 2
## 10 A10 28325 0 A 10 exp190909 20000 2
## # … with 20,246 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[3]] <- dataexp 190921
file <- "Raw_data/plate2/exp_190921/PI_kinetics/190921 HeLa real time cell death assay n4 using 20000 cells .xlsx"
n_skip <- 13
duration <- c(20, 48)
wavelength <- c(493, 535)
# new variables
exp <- "exp190921"
cell_number <- 20e3
plate <- 2
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 19,855 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 1141 0 A 02 exp190921 20000 2
## 2 A03 1128 0 A 03 exp190921 20000 2
## 3 A04 1113 0 A 04 exp190921 20000 2
## 4 A05 1112 0 A 05 exp190921 20000 2
## 5 A06 1140 0 A 06 exp190921 20000 2
## 6 A07 1130 0 A 07 exp190921 20000 2
## 7 A08 1124 0 A 08 exp190921 20000 2
## 8 A09 1129 0 A 09 exp190921 20000 2
## 9 A10 1137 0 A 10 exp190921 20000 2
## 10 A11 1145 0 A 11 exp190921 20000 2
## # … with 19,845 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[4]] <- dataexp 190923
file <- "Raw_data/plate3/exp_190923/PI_kinetics/190923 plate VANANZ 3 HeLa real time cell death n5.xlsx"
n_skip <- 13
duration <- c(22, 18)
wavelength <- 535
# new variables
exp <- "exp190923"
cell_number <- 2e4
plate <- 3
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,280 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 18722 0 A 02 exp190923 20000 3
## 2 A03 19282 0 A 03 exp190923 20000 3
## 3 A04 19248 0 A 04 exp190923 20000 3
## 4 A05 17418 0 A 05 exp190923 20000 3
## 5 A06 19365 0 A 06 exp190923 20000 3
## 6 A07 18733 0 A 07 exp190923 20000 3
## 7 A08 19039 0 A 08 exp190923 20000 3
## 8 A09 19279 0 A 09 exp190923 20000 3
## 9 A10 18530 0 A 10 exp190923 20000 3
## 10 A11 19106 0 A 11 exp190923 20000 3
## # … with 21,270 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[5]] <- dataexp 191107
file <- "Raw_data/plate2/exp_191107/PI_kinetics/191107 plate 2 HeLa 40000 real time cell death .xlsx"
n_skip <- 13
duration <- c(24, 54)
wavelength <- 535
# new variables
exp <- "exp191107"
cell_number <- 4e4
plate <- 2
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 23,750 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 15166 0 A 02 exp191107 40000 2
## 2 A03 15799 0 A 03 exp191107 40000 2
## 3 A04 15422 0 A 04 exp191107 40000 2
## 4 A05 14969 0 A 05 exp191107 40000 2
## 5 A06 15489 0 A 06 exp191107 40000 2
## 6 A07 15563 0 A 07 exp191107 40000 2
## 7 A08 15241 0 A 08 exp191107 40000 2
## 8 A09 14810 0 A 09 exp191107 40000 2
## 9 A10 15169 0 A 10 exp191107 40000 2
## 10 A11 15094 0 A 11 exp191107 40000 2
## # … with 23,740 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[6]] <- dataexp 191109
file <- "Raw_data/plate3/exp_191109/PI_kinetics/Vananz plate 3 191109 real time cell death n1.xlsx"
n_skip <- 13
duration <- c(20, 48)
wavelength <- 535
# new variables
exp <- "exp191109"
cell_number <- 4e4
plate <- 3
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 19,855 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 16534 0 A 02 exp191109 40000 3
## 2 A03 16349 0 A 03 exp191109 40000 3
## 3 A04 16474 0 A 04 exp191109 40000 3
## 4 A05 16186 0 A 05 exp191109 40000 3
## 5 A06 16385 0 A 06 exp191109 40000 3
## 6 A07 16755 0 A 07 exp191109 40000 3
## 7 A08 16924 0 A 08 exp191109 40000 3
## 8 A09 16307 0 A 09 exp191109 40000 3
## 9 A10 15865 0 A 10 exp191109 40000 3
## 10 A11 17343 0 A 11 exp191109 40000 3
## # … with 19,845 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[7]] <- dataexp 191111
file <- "Raw_data/plate3/exp_191111/PI_kinetics/Vananz plate 3 191111 real time cell death n2.xlsx"
n_skip <- 13
duration <- c(21, 36)
wavelength <- 535
# new variables
exp <- "exp191111"
cell_number <- 4e4
plate <- 3
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 20,615 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 16273 0 A 02 exp191111 40000 3
## 2 A03 15536 0 A 03 exp191111 40000 3
## 3 A04 15774 0 A 04 exp191111 40000 3
## 4 A05 16469 0 A 05 exp191111 40000 3
## 5 A06 16403 0 A 06 exp191111 40000 3
## 6 A07 16158 0 A 07 exp191111 40000 3
## 7 A08 16551 0 A 08 exp191111 40000 3
## 8 A09 15644 0 A 09 exp191111 40000 3
## 9 A10 16452 0 A 10 exp191111 40000 3
## 10 A11 16938 0 A 11 exp191111 40000 3
## # … with 20,605 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[8]] <- dataexp 191115
file <- "Raw_data/plate1/exp_191115/PI_kinetics/Vananz plate 1 191115 HeLa 40000 real time cell death assay n1.xlsx"
n_skip <- 13
duration <- c(22, 42)
wavelength <- c(493, 535)
# new variables
exp <- "exp191115"
cell_number <- 4e4
plate <- 1
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,660 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 17160 0 A 02 exp191115 40000 1
## 2 A03 16637 0 A 03 exp191115 40000 1
## 3 A04 17393 0 A 04 exp191115 40000 1
## 4 A05 15767 0 A 05 exp191115 40000 1
## 5 A06 16422 0 A 06 exp191115 40000 1
## 6 A07 16401 0 A 07 exp191115 40000 1
## 7 A08 16895 0 A 08 exp191115 40000 1
## 8 A09 16753 0 A 09 exp191115 40000 1
## 9 A10 16556 0 A 10 exp191115 40000 1
## 10 A11 17113 0 A 11 exp191115 40000 1
## # … with 21,650 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[9]] <- dataexp 191116
file <- "Raw_data/plate1/exp_191116/PI_kinetics/Vananz plate 1 191116 HeLa 40000 real time cell death assay n2.xlsx"
n_skip <- 13
duration <- c(21, 0)
wavelength <- c(493, 535)
# new variables
exp <- "exp191116"
cell_number <- 4e4
plate <- 1
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 20,045 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 18284 0 A 02 exp191116 40000 1
## 2 A03 18787 0 A 03 exp191116 40000 1
## 3 A04 20081 0 A 04 exp191116 40000 1
## 4 A05 16714 0 A 05 exp191116 40000 1
## 5 A06 17366 0 A 06 exp191116 40000 1
## 6 A07 17408 0 A 07 exp191116 40000 1
## 7 A08 17020 0 A 08 exp191116 40000 1
## 8 A09 19013 0 A 09 exp191116 40000 1
## 9 A10 20881 0 A 10 exp191116 40000 1
## 10 A11 20576 0 A 11 exp191116 40000 1
## # … with 20,035 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[10]] <- dataexp 191120
file <- "Raw_data/plate4/exp_191120/PI_kinetics/Vananz plate 4 191120 real time cell death n1.xlsx"
n_skip <- 13
duration <- c(22, 24)
wavelength <- c(493, 535)
# new variables
exp <- "exp191120"
cell_number <- 4e4
plate <- 4
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,375 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 24955 0 A 02 exp191120 40000 4
## 2 A03 23923 0 A 03 exp191120 40000 4
## 3 A04 24598 0 A 04 exp191120 40000 4
## 4 A05 24213 0 A 05 exp191120 40000 4
## 5 A06 24037 0 A 06 exp191120 40000 4
## 6 A07 24919 0 A 07 exp191120 40000 4
## 7 A08 23476 0 A 08 exp191120 40000 4
## 8 A09 24488 0 A 09 exp191120 40000 4
## 9 A10 23964 0 A 10 exp191120 40000 4
## 10 A11 25975 0 A 11 exp191120 40000 4
## # … with 21,365 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[11]] <- dataexp 191121
file <- "Raw_data/plate4/exp_191121/PI_kinetics/Vananz plate 4 191121 real time cell death n2.xlsx"
n_skip <- 13
duration <- c(22, 12)
wavelength <- c(493, 535)
# new variables
exp <- "exp191121"
cell_number <- 4e4
plate <- 4
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,185 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 16341 0 A 02 exp191121 40000 4
## 2 A03 16322 0 A 03 exp191121 40000 4
## 3 A04 16244 0 A 04 exp191121 40000 4
## 4 A05 16695 0 A 05 exp191121 40000 4
## 5 A06 16459 0 A 06 exp191121 40000 4
## 6 A07 16241 0 A 07 exp191121 40000 4
## 7 A08 16206 0 A 08 exp191121 40000 4
## 8 A09 16052 0 A 09 exp191121 40000 4
## 9 A10 15924 0 A 10 exp191121 40000 4
## 10 A11 16305 0 A 11 exp191121 40000 4
## # … with 21,175 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[12]] <- dataexp 191129
file <- "Raw_data/plate5/exp_191129/PI_kinetics/Vananz plate 5 191129 real time cell death n1.xlsx"
n_skip <- 13
duration <- c(19, 12)
wavelength <- c(493, 535)
# new variables
exp <- "exp191129"
cell_number <- 4e4
plate <- 5
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 18,335 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 16672 0 A 02 exp191129 40000 5
## 2 A03 16671 0 A 03 exp191129 40000 5
## 3 A04 17040 0 A 04 exp191129 40000 5
## 4 A05 16557 0 A 05 exp191129 40000 5
## 5 A06 17419 0 A 06 exp191129 40000 5
## 6 A07 16910 0 A 07 exp191129 40000 5
## 7 A08 16963 0 A 08 exp191129 40000 5
## 8 A09 16865 0 A 09 exp191129 40000 5
## 9 A10 17185 0 A 10 exp191129 40000 5
## 10 A11 17426 0 A 11 exp191129 40000 5
## # … with 18,325 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[13]] <- dataexp 191130
file <- "Raw_data/plate5/exp_191130/PI_kinetics/Vananz plate 5 191130 real time cell death n2.xlsx"
n_skip <- 13
duration <- c(24, 48)
wavelength <- c(493, 535)
# new variables
exp <- "exp191130"
cell_number <- 4e4
plate <- 5
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 23,655 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 18720 0 A 02 exp191130 40000 5
## 2 A03 18761 0 A 03 exp191130 40000 5
## 3 A04 18578 0 A 04 exp191130 40000 5
## 4 A05 18881 0 A 05 exp191130 40000 5
## 5 A06 18095 0 A 06 exp191130 40000 5
## 6 A07 18832 0 A 07 exp191130 40000 5
## 7 A08 18985 0 A 08 exp191130 40000 5
## 8 A09 18136 0 A 09 exp191130 40000 5
## 9 A10 19327 0 A 10 exp191130 40000 5
## 10 A11 18031 0 A 11 exp191130 40000 5
## # … with 23,645 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[14]] <- dataexp 191205
file <- "Raw_data/plate6/exp_191205/PI_kinetics/191205 plate vananz 6 HeLa 40000 cell death rate n1.xlsx"
n_skip <- 13
duration <- c(22, 30)
wavelength <- 535
# new variables
exp <- "exp191205"
cell_number <- 4e4
plate <- 6
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 21,470 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 15992 0 A 02 exp191205 40000 6
## 2 A03 16204 0 A 03 exp191205 40000 6
## 3 A04 16689 0 A 04 exp191205 40000 6
## 4 A05 16035 0 A 05 exp191205 40000 6
## 5 A06 16630 0 A 06 exp191205 40000 6
## 6 A07 16469 0 A 07 exp191205 40000 6
## 7 A08 16957 0 A 08 exp191205 40000 6
## 8 A09 16034 0 A 09 exp191205 40000 6
## 9 A10 16141 0 A 10 exp191205 40000 6
## 10 A11 17115 0 A 11 exp191205 40000 6
## # … with 21,460 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[15]] <- dataexp 191206
file <- "Raw_data/plate6/exp_191206/PI_kinetics/191206 plate vananz 6 HeLa 40000 cell death rate n2.xlsx"
n_skip <- 13
duration <- c(24, 36)
wavelength <- 535
# new variables
exp <- "exp191206"
cell_number <- 4e4
plate <- 6
# parse results
data <- parse_kinetics(file = file, duration = duration, wavelength = wavelength, exp = exp, cell_number = cell_number, plate = plate)
data## # A tibble: 23,465 x 9
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A02 18845 0 A 02 exp191206 40000 6
## 2 A03 20015 0 A 03 exp191206 40000 6
## 3 A04 18699 0 A 04 exp191206 40000 6
## 4 A05 18671 0 A 05 exp191206 40000 6
## 5 A06 19672 0 A 06 exp191206 40000 6
## 6 A07 18883 0 A 07 exp191206 40000 6
## 7 A08 18522 0 A 08 exp191206 40000 6
## 8 A09 18891 0 A 09 exp191206 40000 6
## 9 A10 18343 0 A 10 exp191206 40000 6
## 10 A11 19335 0 A 11 exp191206 40000 6
## # … with 23,455 more rows, and 1 more variable: well_id <chr># add to list
kinetics_data[[16]] <- dataMerge the dataframes
kinetics_dat <- bind_rows(kinetics_data)
file <- "Data_parsing/dataframes/all_PI_kinetics.csv"
write_csv(kinetics_dat, file)
# Merge with isolate metadata
# Get pair info (= group)
group_info <- read_csv("plate_info/sample_list_plate.csv") %>%
mutate(sample_id = mdu_id,
strain_group = studyid) %>%
select(sample_id, strain_group)
# Get well info and merge with group info
well_info <- read_csv("plate_info/well_info_n843.csv") %>%
select(well, sample_id, replicate, plate = plate_number) %>%
# We no longer use TOX-5 as positive toxicity control
mutate(sample_id = if_else(sample_id == "TOX-5",
"JE2", sample_id)) %>%
# We use max PI signal (lysis of all cells) instead of total LDH
mutate(sample_id = if_else(sample_id == "Total LDH",
"Complete lysis", sample_id)) %>%
# Replace "blank" with "non infected"
mutate(sample_id = if_else(sample_id == "Blank",
"Non infected", sample_id)) %>%
left_join(group_info) %>%
replace_na(list(strain_group = "CONTROL"))
well_info## # A tibble: 2,976 x 5
## well sample_id replicate plate strain_group
## <chr> <chr> <dbl> <dbl> <chr>
## 1 A01 BPH2722 2 1 VAN-019
## 2 A02 BPH2712 3 1 VAN-010
## 3 A03 BPH2700 1 1 VAN-001
## 4 A04 BPH2711 1 1 VAN-009
## 5 A05 Non infected 3 1 CONTROL
## 6 A06 BPH2714 1 1 VAN-011
## 7 A07 BPH2704 2 1 VAN-004
## 8 A08 BPH2727 1 1 VAN-023
## 9 A09 BPH2719 2 1 VAN-016
## 10 A10 BPH2716 3 1 VAN-013
## # … with 2,966 more rowsdf_kinetics <- kinetics_dat %>%
left_join(well_info)
df_kinetics## # A tibble: 338,081 x 12
## well f_signal timepoint well_row well_col experiment cell_number plate
## <chr> <dbl> <dbl> <chr> <chr> <chr> <dbl> <dbl>
## 1 A01 21309 0 A 01 exp190831 40000 2
## 2 A02 20923 0 A 02 exp190831 40000 2
## 3 A03 19649 0 A 03 exp190831 40000 2
## 4 A04 20962 0 A 04 exp190831 40000 2
## 5 A05 20381 0 A 05 exp190831 40000 2
## 6 A06 20933 0 A 06 exp190831 40000 2
## 7 A07 20737 0 A 07 exp190831 40000 2
## 8 A08 21094 0 A 08 exp190831 40000 2
## 9 A09 20141 0 A 09 exp190831 40000 2
## 10 A10 20781 0 A 10 exp190831 40000 2
## # … with 338,071 more rows, and 4 more variables: well_id <chr>,
## # sample_id <chr>, replicate <dbl>, strain_group <chr>file <- "Data_parsing/dataframes/all_PI_kinetics_well_info.csv"
write_csv(df_kinetics, file)Plot plates
We using a function to plot all replicates together and generate a fitted growth curve.
source("Functions/plot_results.R")
# devtools::install_github("briandconnelly/growthcurve", build_vignettes = TRUE)
# Plot plates
plot_toxicity(df = df_kinetics, plate_number = 2)
plot_toxicity(df = df_kinetics, plate_number = 3)
plot_toxicity(df = df_kinetics, plate_number = 1)
plot_toxicity(df = df_kinetics, plate_number = 4)
plot_toxicity(df = df_kinetics, plate_number = 5)
plot_toxicity(df = df_kinetics, plate_number = 6)